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Yorodumi- PDB-2wy7: Staphylococcus aureus complement subversion protein Sbi-IV in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wy7 | ||||||
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Title | Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement fragment C3d revealing an alternative binding mode | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNE RESPONSE / INNATE IMMUNITY / COMPLEMENT PATHWAY / INFLAMMATORY RESPONSE | ||||||
Function / homology | Function and homology information oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway ...oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / complement activation, classical pathway / Peptide ligand-binding receptors / fatty acid metabolic process / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / G alpha (i) signalling events / blood microparticle / secretory granule lumen / immune response / inflammatory response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Clark, E.A. / Crennell, S. / Upadhyay, A. / Mackay, J.D. / Bagby, S. / van den Elsen, J.M. | ||||||
Citation | Journal: Mol.Immunol. / Year: 2011 Title: A Structural Basis for Staphylococcal Complement Subversion: X-Ray Structure of the Complement- Binding Domain of Staphylococcus Aureus Protein Sbi in Complex with Ligand C3D. Authors: Clark, E.A. / Crennell, S. / Upadhyay, A. / Zozulya, A.V. / Mackay, J.D. / Svergun, D.I. / Bagby, S. / Van Den Elsen, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wy7.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wy7.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 2wy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/2wy7 ftp://data.pdbj.org/pub/pdb/validation_reports/wy/2wy7 | HTTPS FTP |
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-Related structure data
Related structure data | 2wy8C 1c3dS 2hr0 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34746.750 Da / Num. of mol.: 1 / Fragment: C3D, RESIDUES 996-1303 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01024 | ||||
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#2: Protein | Mass: 9256.575 Da / Num. of mol.: 1 / Fragment: SBI-IV, RESIDUES 198-266 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C8LN82 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 100MM TRIS PH8.0, 200MM NACL, 20%(W/V) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9702 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 16, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9702 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→45 Å / Num. obs: 41186 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 96 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3710 / % possible all: 87.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C3D Resolution: 1.7→39.78 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.919 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY HAS THE SAME CRYSTAL DATA AS PDB ENTRY 2WY8. HOWEVER, A SECOND BINDING MODE WAS OBSERVED IN THE CRYSTALLIZED COMPLEX AND THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY HAS THE SAME CRYSTAL DATA AS PDB ENTRY 2WY8. HOWEVER, A SECOND BINDING MODE WAS OBSERVED IN THE CRYSTALLIZED COMPLEX AND THE ASYMMETRIC UNIT WITH THIS (NEW FUNCTIONAL) COMPLEX HAS BEEN REFINED SEPARATELY IN THIS DEPOSITION
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.192 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→39.78 Å
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